EP3673489A4 - Procédés et systèmes de calcul de différences d'énergie libre en utilisant un potentiel de restriction alchimique - Google Patents

Procédés et systèmes de calcul de différences d'énergie libre en utilisant un potentiel de restriction alchimique Download PDF

Info

Publication number
EP3673489A4
EP3673489A4 EP18847675.8A EP18847675A EP3673489A4 EP 3673489 A4 EP3673489 A4 EP 3673489A4 EP 18847675 A EP18847675 A EP 18847675A EP 3673489 A4 EP3673489 A4 EP 3673489A4
Authority
EP
European Patent Office
Prior art keywords
alchemical
systems
methods
free energy
energy differences
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Granted
Application number
EP18847675.8A
Other languages
German (de)
English (en)
Other versions
EP3673489B1 (fr
EP3673489A1 (fr
Inventor
Lingle Wang
Yuqing Deng
Yujie WU
Byungchan Kim
Robert Abel
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Schroedinger Inc
Original Assignee
Schroedinger Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Schroedinger Inc filed Critical Schroedinger Inc
Publication of EP3673489A1 publication Critical patent/EP3673489A1/fr
Publication of EP3673489A4 publication Critical patent/EP3673489A4/fr
Application granted granted Critical
Publication of EP3673489B1 publication Critical patent/EP3673489B1/fr
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/50—Molecular design, e.g. of drugs
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/30—Drug targeting using structural data; Docking or binding prediction
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C10/00—Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like

Landscapes

  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medicinal Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Computing Systems (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Organic Low-Molecular-Weight Compounds And Preparation Thereof (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
EP18847675.8A 2017-08-22 2018-08-21 Procédés et systèmes de calcul de différences d'énergie libre en utilisant un potentiel de restriction alchimique Active EP3673489B1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US15/683,678 US10726946B2 (en) 2017-08-22 2017-08-22 Methods and systems for calculating free energy differences using an alchemical restraint potential
PCT/US2018/047238 WO2019040444A1 (fr) 2017-08-22 2018-08-21 Procédés et systèmes de calcul de différences d'énergie libre en utilisant un potentiel de restriction alchimique

Publications (3)

Publication Number Publication Date
EP3673489A1 EP3673489A1 (fr) 2020-07-01
EP3673489A4 true EP3673489A4 (fr) 2021-05-26
EP3673489B1 EP3673489B1 (fr) 2026-01-14

Family

ID=65434331

Family Applications (1)

Application Number Title Priority Date Filing Date
EP18847675.8A Active EP3673489B1 (fr) 2017-08-22 2018-08-21 Procédés et systèmes de calcul de différences d'énergie libre en utilisant un potentiel de restriction alchimique

Country Status (5)

Country Link
US (2) US10726946B2 (fr)
EP (1) EP3673489B1 (fr)
JP (1) JP7332579B2 (fr)
DK (1) DK3673489T3 (fr)
WO (1) WO2019040444A1 (fr)

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150178442A1 (en) 2013-12-23 2015-06-25 Schrodinger, Inc. Methods and systems for calculating free energy differences using a modified bond stretch potential
US10726946B2 (en) * 2017-08-22 2020-07-28 Schrödinger, Inc. Methods and systems for calculating free energy differences using an alchemical restraint potential
JP7379810B2 (ja) * 2018-08-20 2023-11-15 富士通株式会社 結合自由エネルギーの算出方法、及び算出装置、並びにプログラム
WO2022077258A1 (fr) * 2020-10-14 2022-04-21 深圳晶泰科技有限公司 Procédé de conception de réseau de perturbation d'énergie libre basé sur l'apprentissage automatique
CN112102889B (zh) * 2020-10-14 2024-09-06 深圳晶泰科技有限公司 基于机器学习的自由能微扰网络设计方法
WO2022094870A1 (fr) * 2020-11-05 2022-05-12 深圳晶泰科技有限公司 Procédé de calcul d'énergie libre relative qui est physiquement rigoureux et qui maximise une superposition d'espace de phase
CN112216350B (zh) * 2020-11-05 2022-09-13 深圳晶泰科技有限公司 物理严格且相空间重叠最大化的相对自由能计算方法
US11568961B2 (en) 2020-12-16 2023-01-31 Ro5 Inc. System and method for accelerating FEP methods using a 3D-restricted variational autoencoder
CN114218869B (zh) * 2021-12-21 2025-04-15 深圳晶泰科技有限公司 数据处理方法、装置、模型训练方法和预测自由能方法
CN114360663B (zh) * 2021-12-30 2024-07-02 深圳晶泰科技有限公司 相对结合自由能贡献的确定方法、装置及存储介质

Family Cites Families (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6622094B2 (en) 1996-02-15 2003-09-16 The Trustees Of Columbia University In The City Of New York Method for determining relative energies of two or more different molecules
EP1140737A2 (fr) 1998-12-24 2001-10-10 Harvard University Systeme et procede de conception rationnelle de medicaments sur la base d'une structure faisant intervenir la prediction precise de l'energie libre de liaison
WO2005047520A2 (fr) * 2003-11-07 2005-05-26 Dna Software, Inc. Systeme et methodes d'analyse moleculaire structurelle tridimensionnelle
JP5673245B2 (ja) 2011-03-14 2015-02-18 富士通株式会社 自由エネルギー差予測方法及びシミュレーション装置
US20150317459A1 (en) 2012-12-11 2015-11-05 Asaf FARHI Method to calculate free energies
US20150178442A1 (en) 2013-12-23 2015-06-25 Schrodinger, Inc. Methods and systems for calculating free energy differences using a modified bond stretch potential
ES2977140T3 (es) 2013-12-23 2024-08-19 Schrodinger Inc Métodos y sistemas para calcular diferencias de energía libre usando un potencial de estiramiento de enlace modificado
WO2016052662A1 (fr) 2014-09-30 2016-04-07 国立大学法人大阪大学 Dispositif, procédé, programme et support d'enregistrement sur lequel ledit programme est enregistré permettant de calculer une énergie libre
JP6488728B2 (ja) 2015-01-29 2019-03-27 富士通株式会社 アンカー点の決定方法、結合自由エネルギーの算出方法、及び算出装置、並びにプログラム
JP6489218B2 (ja) 2015-07-23 2019-03-27 富士通株式会社 結合自由エネルギーの算出方法、及び算出装置、並びにプログラム
US10726946B2 (en) * 2017-08-22 2020-07-28 Schrödinger, Inc. Methods and systems for calculating free energy differences using an alchemical restraint potential

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
RINIKER SEREINA ET AL: "Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software", vol. 115, no. 46, 1 November 2011 (2011-11-01), US, pages 13570 - 13577, XP055794936, ISSN: 1520-6106, Retrieved from the Internet <URL:https://pubs.acs.org/doi/pdf/10.1021/jp204303a> DOI: 10.1021/jp204303a *
ROCKLIN GABRIEL J. ET AL: "Separated topologies-A method for relative binding free energy calculations using orientational restraints", vol. 138, no. 8, 28 February 2013 (2013-02-28), US, pages 085104, XP055794911, ISSN: 0021-9606, Retrieved from the Internet <URL:http://dx.doi.org/10.1063/1.4792251> DOI: 10.1063/1.4792251 *
See also references of WO2019040444A1 *
ZHENG LIANQING ET AL: "Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering", JOURNAL OF CHEMICAL THEORY AND COMPUTATION: JCTC, vol. 8, no. 3, 14 February 2012 (2012-02-14), US, pages 810 - 823, XP055794445, ISSN: 1549-9618, DOI: 10.1021/ct200726v *

Also Published As

Publication number Publication date
US20190065697A1 (en) 2019-02-28
DK3673489T3 (da) 2026-04-07
WO2019040444A1 (fr) 2019-02-28
JP7332579B2 (ja) 2023-08-23
JP2020531946A (ja) 2020-11-05
US10726946B2 (en) 2020-07-28
EP3673489B1 (fr) 2026-01-14
EP3673489A1 (fr) 2020-07-01
US20210035660A1 (en) 2021-02-04

Similar Documents

Publication Publication Date Title
EP3673489A4 (fr) Procédés et systèmes de calcul de différences d&#39;énergie libre en utilisant un potentiel de restriction alchimique
EP3645972A4 (fr) Systèmes et procédés de génération de cartes
EP3941249C0 (fr) Dispositif et système de génération d&#39;aérosol comprenant un détecteur de résidus
EP3906508A4 (fr) Systèmes de sécurisation utilisant une intelligence artificielle
EP3758959A4 (fr) Systèmes et procédés de remorquage utilisant la détection magnétique
EP3802374A4 (fr) Systèmes de stockage et de récupération améliorés
EP3632239A4 (fr) Système de charge de dispositif de génération d&#39;aérosol
EP3713446A4 (fr) Brosse à dents suivie et système de suivi de brosse à dents
EP3749604A4 (fr) Systèmes et procédés de stabilité de charge suspendue
EP3724789A4 (fr) Systèmes et procédés de génération d&#39;agent conversationnel
EP3658938A4 (fr) Systèmes et procédés d&#39;utilisation de données de fonctionnement de batterie
EP3405809A4 (fr) Systèmes de télémétrie et de positionnement d&#39;objet et procédés les utilisant
EP3534428A4 (fr) Bloc-batterie, appareil électrique utilisant un bloc-batterie, et système d&#39;appareil électrique
MA50387A (fr) Systèmes et procédés de suivi de transporteurs de marchandises
EP2972921A4 (fr) Technologie informatique mobile, et systèmes et procédés utilisant celle-ci
EP3431229A4 (fr) Dispositif de génération d&#39;information d&#39;action
EP2652649A4 (fr) Procédés et systèmes de calcul incrémental de similarité de sources de données
EP3987308A4 (fr) Systèmes radar et procédés les utilisant
EP4043096A4 (fr) Système de génération de nanobulles utilisant le frottement
EP3625407A4 (fr) Systèmes et procédés d&#39;escalier mobile
PL3890530T3 (pl) Układ wytwarzania aerozolu i wkład z zabezpieczeniem przed wyciekiem
EP3481290A4 (fr) Systèmes et procédés de détection d&#39;un oedème
EP3765822A4 (fr) Systèmes et procédés de génération de carte routière
EP3608939A4 (fr) Générateur de faisceau d&#39;électrons et dispositif d&#39;application de faisceau d&#39;électrons
EP3655988A4 (fr) Dispositif de détection de courant et spectromètre l&#39;utilisant

Legal Events

Date Code Title Description
STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: THE INTERNATIONAL PUBLICATION HAS BEEN MADE

PUAI Public reference made under article 153(3) epc to a published international application that has entered the european phase

Free format text: ORIGINAL CODE: 0009012

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: REQUEST FOR EXAMINATION WAS MADE

17P Request for examination filed

Effective date: 20200323

AK Designated contracting states

Kind code of ref document: A1

Designated state(s): AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR

AX Request for extension of the european patent

Extension state: BA ME

DAV Request for validation of the european patent (deleted)
DAX Request for extension of the european patent (deleted)
A4 Supplementary search report drawn up and despatched

Effective date: 20210423

RIC1 Information provided on ipc code assigned before grant

Ipc: G16C 20/50 20190101AFI20210419BHEP

Ipc: G16B 15/30 20190101ALI20210419BHEP

Ipc: G16C 10/00 20190101ALN20210419BHEP

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: EXAMINATION IS IN PROGRESS

17Q First examination report despatched

Effective date: 20220721

REG Reference to a national code

Ref country code: DE

Ref legal event code: R079

Free format text: PREVIOUS MAIN CLASS: G16B0020400000

Ipc: G16C0020500000

Ref country code: DE

Ref legal event code: R079

Ref document number: 602018088625

Country of ref document: DE

Free format text: PREVIOUS MAIN CLASS: G16B0020400000

Ipc: G16C0020500000

GRAP Despatch of communication of intention to grant a patent

Free format text: ORIGINAL CODE: EPIDOSNIGR1

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: GRANT OF PATENT IS INTENDED

RIC1 Information provided on ipc code assigned before grant

Ipc: G16C 20/50 20190101AFI20250721BHEP

Ipc: G16B 15/30 20190101ALI20250721BHEP

Ipc: G16C 10/00 20190101ALN20250721BHEP

INTG Intention to grant announced

Effective date: 20250805

GRAS Grant fee paid

Free format text: ORIGINAL CODE: EPIDOSNIGR3

GRAA (expected) grant

Free format text: ORIGINAL CODE: 0009210

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: THE PATENT HAS BEEN GRANTED

AK Designated contracting states

Kind code of ref document: B1

Designated state(s): AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR

REG Reference to a national code

Ref country code: CH

Ref legal event code: F10

Free format text: ST27 STATUS EVENT CODE: U-0-0-F10-F00 (AS PROVIDED BY THE NATIONAL OFFICE)

Effective date: 20260114

Ref country code: GB

Ref legal event code: FG4D

REG Reference to a national code

Ref country code: DE

Ref legal event code: R096

Ref document number: 602018088625

Country of ref document: DE

REG Reference to a national code

Ref country code: IE

Ref legal event code: FG4D

P01 Opt-out of the competence of the unified patent court (upc) registered

Free format text: CASE NUMBER: UPC_APP_0003795_3673489/2026

Effective date: 20260202

REG Reference to a national code

Ref country code: DK

Ref legal event code: T3

Effective date: 20260330